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Gradients of Generative Models for Improved Discriminative Analysis of Tandem Mass Spectra
John T Halloran · David M Rocke

Wed Dec 06 05:35 PM -- 05:40 PM (PST) @ Hall C

Tandem mass spectrometry (MS/MS) is a high-throughput technology used to identify the proteins in a complex biological sample, such as a drop of blood. A collection of spectra is generated at the output of the process, each spectrum of which is representative of a peptide (protein subsequence) present in the original complex sample. In this work, we leverage the log-likelihood gradients of generative models to improve the identification of such spectra. In particular, we show that the gradient of a recently proposed dynamic Bayesian network (DBN) may be naturally employed by a kernel-based discriminative classifier. The resulting Fisher kernel substantially improves upon recent attempts to combine generative and discriminative models for post-processing analysis, outperforming all other methods on the evaluated datasets. We extend the improved accuracy offered by the Fisher kernel framework to other search algorithms by introducing Theseus, a DBN representating a large number of widely used MS/MS scoring functions. Furthermore, with gradient ascent and max-product inference at hand, we use Theseus to learn model parameters without any supervision.

Author Information

John T Halloran (University of California, Davis)
David M Rocke (University of California, Davis)

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